From 1972, Bhakdi researched the functioning of the body's non-specific defenses at the Max Planck Institute for Immunobiology in Freiburg. He contributed to a better understanding of the mechanisms with which the large molecules of the complement system in the blood render exogenous substances harmless. In 1978 Bhakdi discovered a protein that attacks and damages cells by sinking into the cell membrane, resulting in the formation of a pore (see membrane attack complex). This was the enforcer molecule of the complement system, which is formed on the surface of foreign cells as a result of a chain reaction involving the immune system. This was followed by the discovery that bacteria, in turn, can also produce pore-forming proteins. Today it is known that the vast majority of pathogenic bacteria produce pore formers that damage host cells. In 1984 the Royal Society in London invited Bhakdi to present the concept of cell membrane damage by pore formers. From then on, Bhakdi concentrated on research on this topic.